RetrogeneDB ID: retro_nleu_2085

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397327.1:8507893..8508921(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: NAP1L1
• Ensembl ID: ENSNLEG00000004682
• Aliases: None
• Description: None

Sequence

>retro_nleu_2085
ATGGCAGACATTGACAACAAAGAACAGTCTAAACTTGATCAAGATTTGGATGATGCTAAAAAAGTAGAAGAAGAAACTGA
TGAAGAAACAAAAATCAAAGCACATCAGCTAACTGTTCAGATGATGCAAAATCCTCAGATTCTTGCAGCCCTTCAAGAAA
GACTTGATGGTCTAATAGAAACACCAACAAGATACATCGAAAGCCTGCCTAGGGTAGTTAAAAAACGAGTAAATGCTCTC
AAAAACCTGTAAGTTAAATGTGCACAGATCGAAGCCAAATTCTATGAGGAAGTTCACAATCTTGAAAGGAAGTATGCTGT
TCTCTGTCAGCCTCTATTTGATAAGCAATTTGAGATTATTAATGCAATTTACAAACCTACAGAAGAAGAATGGGGGCCAG
ATGAAGAAGATGAGATCTCAGAGGAGTTGAAAGAAAAGGCCATGATTGAAGATGAGAAAAAGGATGAAGAAAAAGAAGAT
TCCAAAGGAATTCCTGAATTTTGGTTAACTGTTTTTAAGAATGTTGACTTGTTCAGTGATATGTTTCAGGAACATAATGA
ACCTATTCTGAAGTACTTGAAAGATATTAAAGTGAAGTTCTCAGATGATGGCCAGCCCATGAGTTTTGTCTTAGAATTTC
ACTTTGAAGTGAATGAATATTTTATAAATGAAGTGCTGACAAAGACATATAGCATGAGGTCAGAACCAGATGATTCTGAT
CCCTTTTATTTTGATGGACCAGAAATTATGGGTTTTATAGGGTGCCAGATAGATTGGAAAAAAGAAAGAATATCATTTTG
AAAACCATTAAGAAGAAGCAGAAACACAAGGGACGTGGGACAGTTAGTACTGTCACTAAAACAGTTTCCAATGACTCTTT
CTTTAATTTTTTTGCCCCTCCTGAAGTTTCTGAGAGTGGAGATCTGGATGCTGATGCTAAAACAATCCTTGCTGCAGACT
TTGAAATTGGCCACTTTTTACTGGAGTGTATAATCCCAGGATCAGTGTTATACTTTACTGGAGAAGCT

Alignment

ORF - retro_nleu_2085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.42 %
• Parental protein coverage: 88.49 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADIDNKEQSELDQDLDDVEEVEEEETGEETKIKARQLTVQMMQNPQILAALQERLDGLVETPTGYIESL
          MADIDNKEQS.LDQDLDD...VEEE.T.EETKIKA.QLTVQMMQNPQILAALQERLDGL.ETPT.YIESL
Retrocopy MADIDNKEQSKLDQDLDDAKKVEEE-TDEETKIKAHQLTVQMMQNPQILAALQERLDGLIETPTRYIESL

Parental  PRVVKRRVNALKNLQVKCAQIEAKFYEEVHDLERKYAVLYQPLFDKRFEIINAIYEPTEEECEWKPDEED
          PRVVK.RVNALKNL.VKCAQIEAKFYEEVH.LERKYAVL.QPLFDK.FEIINAIY.PTEEE..W.PDEED
Retrocopy PRVVKKRVNALKNL*VKCAQIEAKFYEEVHNLERKYAVLCQPLFDKQFEIINAIYKPTEEE--WGPDEED

Parental  EISEELKEKAKIEDEKKDEEKEDPKGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFSDAGQPM
          EISE....................KGIPEFWLTVFKNVDL.SDM.QEH.EPILK.LKDIKVKFSD.GQPM
Retrocopy EISEXXXXXXXXXXXXXXXXXXXSKGIPEFWLTVFKNVDLFSDMFQEHNEPILKYLKDIKVKFSDDGQPM

Parental  SFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWK-KGKNVTLKTIKKKQKH
          SFVLEFHFE.NEYF.NEVLTKTY.MRSEPDDSDPF.FDGPEIMG..GCQIDWK.K.KN..LKTIKKKQKH
Retrocopy SFVLEFHFEVNEYFINEVLTKTYSMRSEPDDSDPFYFDGPEIMGFIGCQIDWK<KRKNIILKTIKKKQKH

Parental  KGRGTVRTVTKTVSNDSFFNFFAPPEVPESGDLDDDAEAILAADFEIGHFLRERIIPRSVLYFTGEA
          KGRGTV.TVTKTVSNDSFFNFFAPPEV.ESGDLD.DA..ILAADFEIGHFL.E.IIP.SVLYFTGEA
Retrocopy KGRGTVSTVTKTVSNDSFFNFFAPPEVSESGDLDADAKTILAADFEIGHFLLECIIPGSVLYFTGEA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_2085 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020908	8 retrocopies	retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Callithrix jacchus	ENSCJAG00000001115	1 retrocopy	retro_cjac_534,
Felis catus	ENSFCAG00000000279	1 retrocopy	retro_fcat_1037,
Homo sapiens	ENSG00000187109	3 retrocopies	retro_hsap_1199, retro_hsap_2696, retro_hsap_833,
Gorilla gorilla	ENSGGOG00000003883	3 retrocopies	retro_ggor_1879, retro_ggor_686, retro_ggor_934,
Macropus eugenii	ENSMEUG00000013702	2 retrocopies	retro_meug_1031, retro_meug_604,
Macaca mulatta	ENSMMUG00000015583	1 retrocopy	retro_mmul_233,
Monodelphis domestica	ENSMODG00000020456	4 retrocopies	retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furo	ENSMPUG00000017474	1 retrocopy	retro_mputfur_505,
Mus musculus	ENSMUSG00000058799	1 retrocopy	retro_mmus_263,
Nomascus leucogenys	ENSNLEG00000004682	4 retrocopies	retro_nleu_1192, retro_nleu_2085 , retro_nleu_265, retro_nleu_2766,
Nomascus leucogenys	ENSNLEG00000010841	1 retrocopy	retro_nleu_1876,
Otolemur garnettii	ENSOGAG00000010319	4 retrocopies	retro_ogar_1278, retro_ogar_1281, retro_ogar_3357, retro_ogar_666,
Pan troglodytes	ENSPTRG00000005240	4 retrocopies	retro_ptro_1820, retro_ptro_582, retro_ptro_694, retro_ptro_819,
Rattus norvegicus	ENSRNOG00000003890	1 retrocopy	retro_rnor_150,
Vicugna pacos	ENSVPAG00000007290	3 retrocopies	retro_vpac_435, retro_vpac_441, retro_vpac_601,